Background: Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. Results: Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an FST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness. Conclusions: We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs.
Bibliographical noteFunding Information:
This work was supported by 2-7-10 Agenda Research (PJ00670701) from the National Institute of Animal Science; a grant (PJ008068, PJ008116) from the Next-generation BioGreen 21 Program, Rural Development Administration, Republic of Korea; a grant (2012R1A1A2004932) from the National Research Foundation of Korea and the 2013 Post-doctoral Fellowship Program of the Rural Development Administration, Republic of Korea. We thank two anonymous reviewers for their helpful comments.
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- Directional selection
- Quantitative traits
- Selective sweep